In image-guided percutaneous interventions, a precise planning of the needle path is a key factor to a successful intervention. In this paper we propose a novel method for computing a patient-specific optimal path for such interventions, accounting for both the deformation of the needle and soft tissues due to the insertion of the needle in the body. To achieve this objective, we propose an optimization method for estimating preoperatively a curved trajectory allowing to reach a target even in the case of tissue motion and needle bending. Needle insertions are simulated and regarded as evaluations of the objective function by the iterative planning process. In order to test the planning algorithm, it is coupled with a fast needle insertion simulation involving a flexible needle model and soft tissue finite element modeling, and experimented on the use-case of thermal ablation of liver tumors. Our algorithm has been successfully tested on twelve datasets of patient-specific geometries. Fast convergence to the actual optimal solution has been shown. This method is designed to be adapted to a wide range of percutaneous interventions.

• Klíčová slova
• Biomechanics, Constraint solving, Cryoablation, Deformable models, Finite Element Method (FEM), Flexible needles, Interventional radiology, Optimization, Percutaneous procedures, Radiofrequency ablation, Trajectory planning,
• MeSH
• ablace MeSH
• algoritmy * MeSH
• anatomické modely * MeSH
• chirurgie s pomocí počítače metody   MeSH
• játra patofyziologie   chirurgie   MeSH
• lidé MeSH
• nádory jater chirurgie   MeSH
• počítačová simulace * MeSH
• předoperační období * MeSH
• uživatelské rozhraní počítače MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Image registration methods play a crucial role in computational neuroanatomy. This paper mainly contributes to the field of image registration with the use of nonlinear spatial transformations. Particularly, problems connected to matching magnetic resonance imaging (MRI) brain image data obtained from various subjects and with various imaging conditions are solved here. Registration is driven by local forces derived from multimodal point similarity measures which are estimated with the use of joint intensity histogram and tissue probability maps. A spatial deformation model imitating principles of continuum mechanics is used. Five similarity measures are tested in an experiment with image data obtained from the Simulated Brain Database and a quantitative evaluation of the algorithm is presented. Results of application of the method in automated spatial detection of anatomical abnormalities in first-episode schizophrenia are presented.

• MeSH
• algoritmy * MeSH
• interpretace obrazu počítačem metody   MeSH
• lidé MeSH
• magnetická rezonanční tomografie metody   MeSH
• modely neurologické MeSH
• mozek anatomie a histologie   fyziologie   MeSH
• neuroanatomie metody   MeSH
• neurologie metody   MeSH
• počítačová simulace MeSH
• pružnost MeSH
• psychiatrie metody   MeSH
• reprodukovatelnost výsledků MeSH
• rozpoznávání automatizované metody   MeSH
• senzitivita a specificita MeSH
• subtrakční technika MeSH
• umělá inteligence * MeSH
• vylepšení obrazu metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

A three-dimensional finite element model of a vascular smooth muscle cell is based on models published recently; it comprehends elements representing cell membrane, cytoplasm and nucleus, and a complex tensegrity structure representing the cytoskeleton. In contrast to previous models of eucaryotic cells, this tensegrity structure consists of several parts. Its external and internal parts number 30 struts, 60 cables each, and their nodes are interconnected by 30 radial members; these parts represent cortical, nuclear and deep cytoskeletons, respectively. This arrangement enables us to simulate load transmission from the extracellular space to the nucleus or centrosome via membrane receptors (focal adhesions); the ability of the model was tested by simulation of some mechanical tests with isolated vascular smooth muscle cells. Although material properties of components defined on the basis of the mechanical tests are ambiguous, modelling of different types of tests has shown the ability of the model to simulate substantial global features of cell behaviour, e.g. "action at a distance effect" or the global load-deformation response of the cell under various types of loading. Based on computational simulations, the authors offer a hypothesis explaining the scatter of experimental results of indentation tests.

• MeSH
• analýza metodou konečných prvků MeSH
• biologické modely * MeSH
• buněčný převod mechanických signálů fyziologie   MeSH
• cytoskelet MeSH
• lidé MeSH
• mechanický stres MeSH
• myocyty hladké svaloviny chemie   cytologie   fyziologie   MeSH
• počítačová simulace MeSH
• svaly hladké cévní chemie   cytologie   fyziologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

MOTIVATION: Lipid nanoparticles (LNPs) are the most widely used vehicles for mRNA vaccine delivery. The structure of the lipids composing the LNPs can have a major impact on the effectiveness of the mRNA payload. Several properties should be optimized to improve delivery and expression including biodegradability, synthetic accessibility, and transfection efficiency. RESULTS: To optimize LNPs, we developed and tested models that enable the virtual screening of LNPs with high transfection efficiency. Our best method uses the lipid Simplified Molecular-Input Line-Entry System (SMILES) as inputs to a large language model. Large language model-generated embeddings are then used by a downstream gradient-boosting classifier. As we show, our method can more accurately predict lipid properties, which could lead to higher efficiency and reduced experimental time and costs. AVAILABILITY AND IMPLEMENTATION: Code and data links available at: https://github.com/Sanofi-Public/LipoBART.

• MeSH
• lipidy * chemie   MeSH
• liposomy MeSH
• messenger RNA metabolismus   MeSH
• nanočástice * chemie   MeSH
• transfekce * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Lipid Nanoparticles MeSH Prohlížeč
• lipidy * MeSH
• liposomy MeSH
• messenger RNA MeSH

Cell mechanics are a biophysical indicator of cell state, such as cancer metastasis, leukocyte activation, and cell cycle progression. Atomic force microscopy (AFM) is a widely used technique to measure cell mechanics, where the Young modulus of a cell is usually derived from the Hertz contact model. However, the Hertz model assumes that the cell is an elastic, isotropic, and homogeneous material and that the indentation is small compared to the cell size. These assumptions neglect the effects of the cytoskeleton, cell size and shape, and cell environment on cell deformation. In this study, we investigated the influence of cell size on the estimated Young's modulus using liposomes as cell models. Liposomes were prepared with different sizes and filled with phosphate buffered saline (PBS) or hyaluronic acid (HA) to mimic the cytoplasm. AFM was used to obtain the force indentation curves and fit them to the Hertz model. We found that the larger the liposome, the lower the estimated Young's modulus for both PBS-filled and HA-filled liposomes. This suggests that the Young modulus obtained from the Hertz model is not only a property of the cell material but also depends on the cell dimensions. Therefore, when comparing or interpreting cell mechanics using the Hertz model, it is essential to account for cell size.

• Klíčová slova
• Hertz contact model, atomic force microscopy (AFM), cell mechanics, cell stiffness,
• MeSH
• biologické modely MeSH
• biomechanika MeSH
• kyselina hyaluronová chemie   MeSH
• lidé MeSH
• liposomy * chemie   MeSH
• mikroskopie atomárních sil * metody   MeSH
• modul pružnosti * MeSH
• velikost buňky MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kyselina hyaluronová MeSH
• liposomy * MeSH

Experimental teratogenic models of the campomelic syndrome in duck and chick embryos and in frog tadpoles are presented. The association of selective growth impairment of the peripheral and facial nerve trunks including the spinal cord and nerve roots is suggested as an underlying cause for adaptive shortening of the corresponding skeletal parts. Buckling may occur because the growing bones tend to accommodate to these underdeveloped neurological structures even at the cost of a deformity. It is suggested that investigation of the effects of "skeletal" teratogens upon the nervous system may be more logical than concentrating upon bone growth which may be the secondary effect.

• MeSH
• abnormality vyvolané léky diagnostické zobrazování   MeSH
• kachny MeSH
• karcinogeny MeSH
• kosti a kostní tkáň abnormality   diagnostické zobrazování   MeSH
• kuřecí embryo MeSH
• poruchy růstu diagnostické zobrazování   MeSH
• radiografie MeSH
• Ranidae MeSH
• rodenticidy MeSH
• syndrom MeSH
• teratogeny * MeSH
• zvířata MeSH
• Check Tag
• kuřecí embryo MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• karcinogeny MeSH
• rodenticidy MeSH
• teratogeny * MeSH

A fast and accurate fusion of intra-operative images with a pre-operative data is a key component of computer-aided interventions which aim at improving the outcomes of the intervention while reducing the patient's discomfort. In this paper, we focus on the problematic of the intra-operative navigation during abdominal surgery, which requires an accurate registration of tissues undergoing large deformations. Such a scenario occurs in the case of partial hepatectomy: to facilitate the access to the pathology, e.g. a tumor located in the posterior part of the right lobe, the surgery is performed on a patient in lateral position. Due to the change in patient's position, the resection plan based on the pre-operative CT scan acquired in the supine position must be updated to account for the deformations. We suppose that an imaging modality, such as the cone-beam CT, provides the information about the intra-operative shape of an organ, however, due to the reduced radiation dose and contrast, the actual locations of the internal structures necessary to update the planning are not available. To this end, we propose a method allowing for fast registration of the pre-operative data represented by a detailed 3D model of the liver and its internal structure and the actual configuration given by the organ surface extracted from the intra-operative image. The algorithm behind the method combines the iterative closest point technique with a biomechanical model based on a co-rotational formulation of linear elasticity which accounts for large deformations of the tissue. The performance, robustness and accuracy of the method is quantitatively assessed on a control semi-synthetic dataset with known ground truth and a real dataset composed of nine pairs of abdominal CT scans acquired in supine and flank positions. It is shown that the proposed surface-matching method is capable of reducing the target registration error evaluated of the internal structures of the organ from more than 40 mm to less then 10 mm. Moreover, the control data is used to demonstrate the compatibility of the method with intra-operative clinical scenario, while the real datasets are utilized to study the impact of parametrization on the accuracy of the method. The method is also compared to a state-of-the art intensity-based registration technique in terms of accuracy and performance.

• Klíčová slova
• Computer-aided interventions, Deformable image registration, Finite element method, Human liver,
• MeSH
• algoritmy MeSH
• analýza metodou konečných prvků MeSH
• biomechanika MeSH
• břicho diagnostické zobrazování   chirurgie   MeSH
• chirurgie s pomocí počítače metody   MeSH
• elastografie * MeSH
• lidé MeSH
• nemoci jater diagnostické zobrazování   chirurgie   MeSH
• peroperační doba MeSH
• počítačová rentgenová tomografie * MeSH
• počítačová simulace MeSH
• počítačová tomografie s kuželovým svazkem * MeSH
• polohování pacienta MeSH
• rentgenový obraz - interpretace počítačová metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH

A novel biofilm model is described which systemically couples bacteria, extracellular polymeric substances (EPS) and solvent phases in biofilm. This enables the study of contributions of rheology of individual phases to deformation of biofilm in response to fluid flow as well as interactions between different phases. The model, which is based on first and second laws of thermodynamics, is derived using an energetic variational approach and phase-field method. Phase-field coupling is used to model structural changes of a biofilm. A newly developed unconditionally energy-stable numerical splitting scheme is implemented for computing the numerical solution of the model efficiently. Model simulations predict biofilm cohesive failure for the flow velocity between [Formula: see text] and [Formula: see text] m s(-1) which is consistent with experiments. Simulations predict biofilm deformation resulting in the formation of streamers for EPS exhibiting a viscous-dominated mechanical response and the viscosity of EPS being less than [Formula: see text]. Higher EPS viscosity provides biofilm with greater resistance to deformation and to removal by the flow. Moreover, simulations show that higher EPS elasticity yields the formation of streamers with complex geometries that are more prone to detachment. These model predictions are shown to be in qualitative agreement with experimental observations.

• Klíčová slova
• biofilm, continuum mechanics, detachment, energetic variation, phase-field model, viscoelasticity,
• MeSH
• Bacteria cytologie   MeSH
• bakteriální adheze fyziologie   MeSH
• bakteriální polysacharidy metabolismus   MeSH
• biofilmy růst a vývoj   MeSH
• biologické modely * MeSH
• fyziologie bakterií MeSH
• mechanický stres MeSH
• mikrofluidika metody   MeSH
• modul pružnosti fyziologie   MeSH
• pevnost ve smyku fyziologie   MeSH
• počítačová simulace MeSH
• velikost buňky MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• bakteriální polysacharidy MeSH

PURPOSE OF THE STUDY We hypothesized that preoperative planning with 3D modeling of complex foot deformities would be useful for the education of orthopedics and traumatology residents. MATERIAL AND METHODS This study is prospectively designed study with a control group. Twenty eight residents (study group) who assisted the surgeons during the interventions and ten senior surgeons (control group) were included in the study. All participants assessed virtual 3D-CT images and videos of the cases before the surgery. Ten adult cases of foot bone deformities were evaluated. 3D-CT reconstruction was performed and a 3D model of each deformity was created using the hospital's picture archiving and communication system. The completed 3D models were sterilized in hydrogen peroxide and put on the surgical table in a sterile manner. After surgery, the residents (group I) and surgeons (group II) were questioned regarding their satisfaction with 3D modeling. Responses were structured by a five-point Likert scale (1, strongly disagree; 2, disagree; 3, neither agree nor disagree; 4, agree; and 5, strongly agree). RESULTS The surgeons (group II, n = 10) were satisfied with the sterilized 3D models, which they could touch and re-examine on the operating table. The residents (group I, n = 28) were significantly more satisfied than the senior surgeons (p=0.01). The 3D modeling met both the surgeons' and residents' expectations. DISCUSSION The survey results for the surgeons (group II) were satisfied with the sterilized 3D models, which they could touch and reexamine on the operating table (question 3). They gave the best scores (mean, 4.8/5) for clarity of the 3D model. On the other hand, they gave the lowest scores (mean 3.1/5) to 3D models due to its contribution in understanding deformity over virtual 3D-CT evaluations (question 2 and 5). The residents (group I) differed from those for the senior surgeons. Residents gave the highest scores for understanding of the deformity (question 2 and 5) and clarity (question 1). These outcomes may be interpreted to indicate i) that 3D modeling may be used for education, and ii) that younger surgeons are more interested in novel technological developments. Therefore, the outcomes did differ significantly between the senior surgeons and residents (Table 1). These outcomes may be explicated as; 3D modeling of the foot deformities may not be mandatory for the experienced surgeons for understanding the deformity. On the other hand 3D modeling would be useful tools for younger surgeons and for their education. CONCLUSIONS 3D modeling of foot deformities is more informative than virtual 3D videos. However, with consideration of costs and long processing times, 3D printing may be used optimally for rare deformities. When considering the role of touch sense in surgical learning, 3D modeling gives more detailed and more satisfactory planning than virtual 3D videos. 3D modeling is more useful for young surgeons, and it will be used mainly for education in the future. Key words: 3D printing, deformity, foot and ankle, simulation.

• MeSH
• 3D tisk MeSH
• chirurgové * MeSH
• deformity nohy (od hlezna dolů) * MeSH
• dospělí MeSH
• lidé MeSH
• ortopedie * MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Soliton dynamics and nonlinear phenomena in quantum deformation has been investigated through conformal time differential generalized form of q deformed Sinh-Gordon equation. The underlying equation has recently undergone substantial amount of research. In Phase 1, we employed modified auxiliary and new direct extended algebraic methods. Trigonometric, hyperbolic, exponential and rational solutions are successfully extracted using these techniques, coupled with the best possible constraint requirements implemented on parameters to ensure the existence of solutions. The findings, then, are represented by 2D, 3D and contour plots to highlight the various solitons' propagation patterns such as kink-bright, bright, dark, bright-dark, kink, and kink-peakon solitons and solitary wave solutions. It is worth emphasizing that kink dark, dark peakon, dark and dark bright solitons have not been found earlier in literature. In phase 2, the underlying model is examined under various chaos detecting tools for example lyapunov exponents, multistability and time series analysis and bifurcation diagram. Chaotic behavior is investigated using various initial condition and novel results are obtained.

• MeSH
• algoritmy MeSH
• kvantová teorie * MeSH
• nelineární dynamika * MeSH
• počítačová simulace MeSH
• teoretické modely MeSH
• Publikační typ
• časopisecké články MeSH